I see the GOP massively tying itself in knots because Trump is really, really NOT the person they wanted and populism is NOT the direction anyone really wants to go. The Democrats have a similar problem, but to a much lesser extent as Hillary is an insider so generally accepted but she's still very much on the populist bandwagon as opposed to Sanders (and others).

Is there a real chance for a GOP disintegration forming a legitimate party with a Democratic splinter group, and forcing a chaotic three party race for a few cycles, or will we see both parties reform around different battle lines when the dust settles in a few cycles time?

In my mind, this is Hillary's election to lose now, but the power players from both sides will be looking strongly at control in the future. Populism is too chaotic to control...

No you won't, because unless the Democrats and Republicans move MUCH farther left and right respectively necessitating the formation of a moderate party, only the Democrats or Republican candidates will win (depending on which party fractures).